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Zanditenas E, Ankri S. Unraveling the interplay between unicellular parasites and bacterial biofilms: Implications for disease persistence and antibiotic resistance. Virulence 2024; 15:2289775. [PMID: 38058008 PMCID: PMC10761080 DOI: 10.1080/21505594.2023.2289775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Bacterial biofilms have attracted significant attention due to their involvement in persistent infections, food and water contamination, and infrastructure corrosion. This review delves into the intricate interactions between bacterial biofilms and unicellular parasites, shedding light on their impact on biofilm formation, structure, and function. Unicellular parasites, including protozoa, influence bacterial biofilms through grazing activities, leading to adaptive changes in bacterial communities. Moreover, parasites like Leishmania and Giardia can shape biofilm composition in a grazing independent manner, potentially influencing disease outcomes. Biofilms, acting as reservoirs, enable the survival of protozoan parasites against environmental stressors and antimicrobial agents. Furthermore, these biofilms may influence parasite virulence and stress responses, posing challenges in disease treatment. Interactions between unicellular parasites and fungal-containing biofilms is also discussed, hinting at complex microbial relationships in various ecosystems. Understanding these interactions offers insights into disease mechanisms and antibiotic resistance dissemination, paving the way for innovative therapeutic strategies and ecosystem-level implications.
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Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
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2
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Wang X, Ganzert L, Bartholomäus A, Amen R, Yang S, Guzmán CM, Matus F, Albornoz MF, Aburto F, Oses-Pedraza R, Friedl T, Wagner D. The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173846. [PMID: 38871316 DOI: 10.1016/j.scitotenv.2024.173846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.
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Affiliation(s)
- Xiuling Wang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Lars Ganzert
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Rahma Amen
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; Department of Zoology, Faculty of Science, Aswan University, 81528 Aswan, Egypt
| | - Sizhong Yang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Carolina Merino Guzmán
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, BIOREN, Universidad de La Frontera, Temuco 4780000, Chile
| | - Francisco Matus
- Laboratory of Conservation and Dynamics of Volcanic Soils, Department of Chemical Sciences and Natural Resources, Universidad de La Frontera, Temuco 4780000, Chile; Network for Extreme Environmental Research (NEXER), Universidad de La Frontera, Temuco 4780000, Chile
| | - Maria Fernanda Albornoz
- Laboratorio de Investigación de Suelos, Aguas y Bosques (LISAB), Universidad de Concepción, Concepción, Chile
| | - Felipe Aburto
- Pedology and Soil Biogeochemistry Lab, Soil and Crop Sciences Department, Texas A&M University, College Station, TX, USA
| | - Rómulo Oses-Pedraza
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama, Universidad de Atacama (CRIDESAT UDA), Copayapu 484, Copiapó 1530000, Chile
| | - Thomas Friedl
- Department of Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University, 37073 Göttingen, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany.
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Diaz-Mateus MA, Salgar-Chaparro SJ, Tarazona J, Farhat H. Exploring the influence of deposit mineral composition on biofilm communities in oil and gas systems. Front Microbiol 2024; 15:1438806. [PMID: 39139372 PMCID: PMC11319257 DOI: 10.3389/fmicb.2024.1438806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024] Open
Abstract
Introduction Inside oil and gas pipelines, native microbial communities and different solid compounds typically coexist and form mixed deposits. However, interactions between these deposits (primarily consisting of mineral phases) and microorganisms in oil and gas systems remain poorly understood. Here, we investigated the influence of magnetite (Fe3O4), troilite (FeS), and silica (SiO2) on the microbial diversity, cell viability, biofilm formation, and EPS composition of an oil-recovered multispecies consortium. Methods An oilfield-recovered microbial consortium was grown for 2 weeks in separate bioreactors, each containing 10 g of commercially available magnetite (Fe3O4), troilite (FeS), or silica (SiO2) at 40°C ± 1°C under a gas atmosphere of 20% CO2/80% N2. Results The microbial population formed in troilite significantly differed from those in silica and magnetite, which exhibited significant similarities. The dominant taxa in troilite was the Dethiosulfovibrio genus, whereas Sulfurospirillum dominated in magnetite and silica. Nevertheless, biofilm formation was lowest on troilite and highest on silica, correlating with the observed cell viability. Discussion The dissolution of troilite followed by the liberation of HS- (H2S) and Fe2+ into the test solution, along with its larger particle size compared to silica, likely contributed to the observed results. Confocal laser scanning microscopy revealed that the EPS of the biofilm formed in silica was dominated by eDNA, while those in troilite and magnetite primarily contained polysaccharides. Although the mechanisms of this phenomenon could not be determined, these findings are anticipated to be particularly valuable for enhancing MIC mitigation strategies currently used in oil and gas systems.
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Affiliation(s)
- Maria A. Diaz-Mateus
- WA School of Mines: Minerals, Energy and Chemical Engineering, Curtin Corrosion Centre, Curtin University, Bentley, WA, Australia
| | - Silvia J. Salgar-Chaparro
- WA School of Mines: Minerals, Energy and Chemical Engineering, Curtin Corrosion Centre, Curtin University, Bentley, WA, Australia
| | - Johanna Tarazona
- WA School of Mines: Minerals, Energy and Chemical Engineering, Curtin Corrosion Centre, Curtin University, Bentley, WA, Australia
| | - Hanan Farhat
- Qatar Environment and Energy Research Institute (QEERI), Doha, Qatar
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Puvvula PK, Johnson A, Bernal-Mizrachi L. Unveiling retrotransposon-derived DNA zip code for myeloma cell internalization. Oncoscience 2024; 11:58-64. [PMID: 39015604 PMCID: PMC11251427 DOI: 10.18632/oncoscience.606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
| | - Anthony Johnson
- Kodikaz Therapeutic Solutions, (INC), New York, NY 10014, USA
| | - Leon Bernal-Mizrachi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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Tetz V, Kardava K, Vecherkovskaya M, Khodadadi-Jamayran A, Tsirigos A, Tetz G. Previously unknown regulatory role of extracellular RNA on bacterial directional migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603110. [PMID: 39026763 PMCID: PMC11257571 DOI: 10.1101/2024.07.11.603110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Bacterial directional migration plays a significant role in bacterial adaptation. However, the regulation of this process, particularly in young biofilms, remains unclear. Here, we demonstrated the critical role of extracellular RNA as part of the Universal Receptive System in bacterial directional migration using a multidisciplinary approach, including bacterial culture, biochemistry, and genetics. We found that the destruction or inactivation of extracellular RNA with RNase or RNA-specific antibodies in the presence of the chemoattractant triggered the formation of bacterial "runner cells» in what we call a "panic state" capable of directional migration. These cells quickly migrated even on the surface of 1.5% agar and formed evolved colonies that were transcriptionally and biochemically different from the ancestral cells. We have also shown that cell-free DNA from blood plasma can act as a potent bacterial chemoattractant. Our data revealed a previously unknown role of bacterial extracellular RNA in the regulation of bacterial migration and have shown that its destruction or inhibition triggered the directional migration of developing and mature biofilms towards the chemoattractant.
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Mahmud HA, Garcia R, Garcia A, Baishya J, Wakeman CA. Rescue of pyrimidine-defective Pseudomonas aeruginosa through metabolic complementation. Microbiol Spectr 2024; 12:e0422623. [PMID: 38990029 PMCID: PMC11302043 DOI: 10.1128/spectrum.04226-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Chronic infections harbor multiple pathogens where dynamic interactions between members of the polymicrobial community play a major role in determining the infection outcome. For example, in a nutrient-rich polymicrobial infection, bacteria have the potential to undergo evolutionary changes that impair their ability to synthesize essential metabolites. This adaptation may facilitate metabolic interdependencies between neighboring pathogens and lead to difficult-to-treat chronic infections. Our research group previously demonstrated that Pseudomonas aeruginosa (PA) and Staphylococcus aureus (SA), typically considered classical competitors, can adopt a cooperative lifestyle through bi-directional purine exchange medicated by exogenous DNA (eDNA) release. To further validate our initial findings, in this study, we investigated the potential exchange of pyrimidine between PA and other pathogens, which is another constituent of DNA. In our findings, we observed that a pyrimidine-deficient transposon mutant strain of PA showed improved growth when co-cultured with wild-type PA, SA, Acinetobacter baumannii (AB), and Enterococcus faecalis (EF). Additionally, improved fitness of pyrimidine-deficient PA was further observed in chemical complementation with eDNA and uridine-5'-monophosphate. Interestingly, the rescue of PA growth through eDNA complementation is not as effective as in intact cells, such as SA, AB, EF, and wild-type PA, implying that eDNA is a lesser contributor to this metabolic complementation. Also, the exchange mechanism between pathogens involves more active mechanisms beyond simple eDNA or metabolite release. Our data further highlights the importance of cell-to-cell contact for effective and increased metabolic complementation. IMPORTANCE This research holds crucial implications for combating chronic infections, where multiple pathogens coexist and interact within the same environment. By uncovering the dynamic exchange of pyrimidines between Pseudomonas aeruginosa (PA) and Staphylococcus aureus (SA), our study reveals a previously unrecognized aspect of interspecies cooperation. The observed enhanced growth of a pyrimidine-deficient PA strain when co-cultured with SA suggests potential avenues for understanding and disrupting bacterial metabolic interdependencies in chronic infection settings. Furthermore, our findings highlight the mechanisms involved in metabolic exchange, emphasizing the importance of cell-to-cell contact. This research explored essential metabolic interactions to address the challenges posed by difficult-to-treat chronic infections.
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Affiliation(s)
- Hafij Al Mahmud
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Randy Garcia
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Alexsis Garcia
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Jiwasmika Baishya
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
- The Assam Royal Global University, Guwahati, Assam, India
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7
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Wang S, Tian R, Bi Y, Meng F, Zhang R, Wang C, Wang D, Liu L, Zhang B. A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems. CHEMOSPHERE 2024; 359:142264. [PMID: 38714248 DOI: 10.1016/j.chemosphere.2024.142264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 05/09/2024]
Abstract
Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.
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Affiliation(s)
- Shaopo Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Ruimin Tian
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Yanmeng Bi
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Fansheng Meng
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Rui Zhang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Chenchen Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Dong Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Lingjie Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China.
| | - Bo Zhang
- Tianjin Eco-City Water Investment and Construction Co. Ltd, Hexu Road 276, Tianjin, 300467, China
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Lin Q, Sheng M, Kang Z, Xu J, Gao Y, Ma S, Xin B, Tan Y. Synergistic and antibiofilm activity of DNase I and glucose oxidase loaded chitosan nanoparticles against dual-species biofilms of Listeria monocytogenes and Salmonella. Int J Biol Macromol 2024; 269:131943. [PMID: 38688332 DOI: 10.1016/j.ijbiomac.2024.131943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 03/28/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Salmonella and Listeria monocytogenes are two of the most common foodborne pathogens in the food industry. They form dual-species biofilms, which have a higher sensitivity to antimicrobial treatment and a greater microbial adhesion. In this experiment, we loaded DNase I and glucose oxidase (GOX) on chitosan nanoparticles (CSNPs) to explore their inhibitory effects on and disruption of dual-species biofilms of Salmonella enterica and L. monocytogenes. Transmission electron microscopy (TEM) showed that CSNP-DNase-GOX and CSNPs were spherical in shape. CSNP-DNase-GOX was shifted and altered compared to the infrared peaks of CSNPs. CSNPs loaded with DNase I and GOX showed an increase in the particle size and an alteration in the polydispersity index (PDI) and the zeta potential. Compared to free DNase I or GOX, DNase I and GOX loaded on CSNPs had higher stability at different temperatures. CSNP-DNase-GOX was more effective in inhibiting dual-species biofilms than CSNP-GOX. Scanning electron microscopy (SEM) and fluorescence microscopy were used to observe the structure of the biofilm, which further illustrated that CSNP-DNase-GOX disrupted the dual-species biofilms of S. enterica and L. monocytogenes.
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Affiliation(s)
- Quan Lin
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China; Shandong Technology Innovation Center of Special Food, Qingdao, China; Qingdao Special Food Research Institute, Qingdao, China
| | - Maokun Sheng
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China; Shandong Technology Innovation Center of Special Food, Qingdao, China; Qingdao Special Food Research Institute, Qingdao, China
| | - Zhaodi Kang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China; Shandong Technology Innovation Center of Special Food, Qingdao, China; Qingdao Special Food Research Institute, Qingdao, China
| | - Jiaman Xu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China; Shandong Technology Innovation Center of Special Food, Qingdao, China; Qingdao Special Food Research Institute, Qingdao, China
| | - Yan Gao
- Marine Science Research Institute of Shandong Province (National Oceanographic Center of Qingdao), Qingdao, China
| | - Su Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Bingchang Xin
- Department of Cariology and Endodontology, Qingdao Stomatological Hospital Affiliated to Qingdao University, Qingdao, China
| | - Yulong Tan
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China; Shandong Technology Innovation Center of Special Food, Qingdao, China; Qingdao Special Food Research Institute, Qingdao, China.
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9
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Shapiro JA. A very brief note on why bacterial evolution has physiology. J Physiol 2024; 602:2395-2399. [PMID: 37641409 DOI: 10.1113/jp284409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
The majority of bacteria live and evolve in surface biofilms. Both growth in biofilms and horizontal transfer of DNA are regulated by quorum-sensing pheromone signals. The common regulation of bacterial surface growth and DNA transfers illustrates how physiology contributes to bacterial evolution.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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10
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Sharma DK, Rajpurohit YS. Multitasking functions of bacterial extracellular DNA in biofilms. J Bacteriol 2024; 206:e0000624. [PMID: 38445859 PMCID: PMC11025335 DOI: 10.1128/jb.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.
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Affiliation(s)
- Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
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Meliefste HM, Mudde SE, Ammerman NC, de Steenwinkel JEM, Bax HI. A laboratory perspective on Mycobacterium abscessus biofilm culture, characterization and drug activity testing. Front Microbiol 2024; 15:1392606. [PMID: 38690364 PMCID: PMC11058659 DOI: 10.3389/fmicb.2024.1392606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Mycobacterium abscessus is an emerging opportunistic pathogen causing severe pulmonary infections in patients with underlying lung disease and cystic fibrosis in particular. The rising prevalence of M. abscessus infections poses an alarming threat, as the success rates of available treatment options are limited. Central to this challenge is the absence of preclinical in vitro models that accurately mimic in vivo conditions and that can reliably predict treatment outcomes in patients. M. abscessus is notorious for its association with biofilm formation within the lung. Bacteria in biofilms are more recalcitrant to antibiotic treatment compared to planktonic bacteria, which likely contributes to the lack of correlation between preclinical drug activity testing (typically performed on planktonic bacteria) and treatment outcome. In recent years, there has been a growing interest in M. abscessus biofilm research. However, the absence of standardized methods for biofilm culture, biofilm characterization and drug activity testing has led to a wide spectrum of, sometimes inconsistent, findings across various studies. Factors such as strain selection, culture medium, and incubation time hugely impact biofilm development, phenotypical characteristics and antibiotic susceptibility. Additionally, a broad range of techniques are used to study M. abscessus biofilms, including quantification of colony-forming units, crystal violet staining and fluorescence microscopy. Yet, limitations of these techniques and the selected readouts for analysis affect study outcomes. Currently, research on the activity of conventional antibiotics, such as clarithromycin and amikacin, against M. abscessus biofilms yield ambiguous results, underscoring the substantial impact of experimental conditions on drug activity assessment. Beyond traditional drug activity testing, the exploration of novel anti-biofilm compounds and the improvement of in vitro biofilm models are ongoing. In this review, we outline the laboratory models, experimental variables and techniques that are used to study M. abscessus biofilms. We elaborate on the current insights of M. abscessus biofilm characteristics and describe the present understanding of the activity of traditional antibiotics, as well as potential novel compounds, against M. abscessus biofilms. Ultimately, this work contributes to the advancement of fundamental knowledge and practical applications of accurate preclinical M. abscessus models, thereby facilitating progress towards improved therapies for M. abscessus infections.
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Affiliation(s)
| | - Saskia Emily Mudde
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Nicole Christine Ammerman
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Hannelore Iris Bax
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
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12
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Wang X, Chi Y, Song S. Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review. Front Microbiol 2024; 15:1347745. [PMID: 38591030 PMCID: PMC10999704 DOI: 10.3389/fmicb.2024.1347745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.
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Affiliation(s)
| | - Yongkuan Chi
- School of Karst Science, State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
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Stelmaszyk L, Stange C, Hügler M, Sidhu JP, Horn H, Tiehm A. Quantification of β-lactamase producing bacteria in German surface waters with subsequent MALDI-TOF MS-based identification and β-lactamase activity assay. Heliyon 2024; 10:e27384. [PMID: 38486766 PMCID: PMC10937694 DOI: 10.1016/j.heliyon.2024.e27384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Environmental oligotrophic bacteria are suspected to be highly relevant carriers of antimicrobial resistance (AMR). However, there is a lack of validated methods for monitoring in the aquatic environment. Since extended-spectrum β-lactamases (ESBLs) play a particularly important role in the clinical sector, a culturing method based on R2A-medium spiked with different combinations of β-lactams was applied to quantify β-lactamase-producing environmental bacteria from surface waters. In German surface water samples (n = 28), oligotrophic bacteria ranging from 4.0 × 103 to 1.7 × 104 CFU per 100 mL were detected on the nutrient-poor medium spiked with 3rd generation cephalosporins and carbapenems. These numbers were 3 log10 higher compared to ESBL-producing Enterobacteriales of clinical relevance from the same water samples. A MALDI-TOF MS identification of the isolates demonstrated, that the method leads to the isolation of environmentally relevant strains with Pseudomonas, Flavobacterium, and Janthinobacterium being predominant β-lactam resistant genera. Subsequent micro-dilution antibiotic susceptibility tests (Micronaut-S test) confirmed the expression of β-lactamases. The qPCR analysis of surface waters DNA extracts showed the presence of β-lactamase genes (blaTEM, blaCMY-2, blaOXA-48, blaVIM-2, blaSHV, and blaNDM-1) at concentrations of 3.7 (±1.2) to 1.0 (±1.9) log10 gene copies per 100 mL. Overall, the results demonstrate a widespread distribution of cephalosporinase and carbapenemase enzymes in oligotrophic environmental bacteria that have to be considered as a reservoir of ARGs and contribute to the spread of antibiotic resistance.
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Affiliation(s)
- Lara Stelmaszyk
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
| | - Claudia Stange
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
| | - Michael Hügler
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
| | - Jatinder P.S. Sidhu
- CSIRO Oceans and Atmosphere, Ecosciences Precinct, 41 Boggo Road, Brisbane, Australia
| | - Harald Horn
- Karlsruher Institut für Technologie, Engler-Bunte Institute, Wasserchemie und Wassertechnologie, Engler-Bunte-Ring 9a, Karlsruhe, Germany
| | - Andreas Tiehm
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
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14
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Bai Y, Lin H, Wang C, Wang Q, Qu J. Digitalizing river aquatic ecosystems. J Environ Sci (China) 2024; 137:677-680. [PMID: 37980050 DOI: 10.1016/j.jes.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 11/20/2023]
Abstract
Traditional river health assessment relies on limited water quality indices and representative organism activity, but does not comprehensively obtain biotic and abiotic information of the ecosystem. Here, we propose a new approach to evaluate the ecological and health risks of river aquatic ecosystems. First, detailed physicochemical and biological characterization of a river ecosystem can be obtained through pollutant determination (especially emerging pollutants) and DNA/RNA sequencing. Second, supervised machine learning can be applied to perform classification analysis of characterization data and ascertain river ecosystem ecology and health. Our proposed methodology transforms river ecosystem health assessment and can be applied in river management.
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Affiliation(s)
- Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hui Lin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenchen Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China
| | - Qiaojuan Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, Tsinghua University, Beijing 100084, China.
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15
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Ma Y, Tang WS, Liu SY, Khoo BL, Chua SL. Juglone as a Natural Quorum Sensing Inhibitor against Pseudomonas aeruginosa pqs-Mediated Virulence and Biofilms. ACS Pharmacol Transl Sci 2024; 7:533-543. [PMID: 38357290 PMCID: PMC10863437 DOI: 10.1021/acsptsci.3c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Pseudomonas aeruginosa is a notorious opportunistic pathogen associated with chronic biofilm-related infections, posing a significant challenge to effective treatment strategies. Quorum sensing (QS) and biofilm formation are critical virulence factors employed by P. aeruginosa, contributing to its pathogenicity and antibiotic resistance. Other than the homoserine-based QS systems, P. aeruginosa also possesses the quinolone-based Pseudomonas quinolone signal (PQS) QS signaling. Synthesis of the PQS signaling molecule is achieved by the pqsABCDEH operon, whereas the PQS signaling response was mediated by the PqsR receptor. In this study, we report the discovery of a novel natural compound, Juglone, with potent inhibitory effects on pqs QS and biofilm formation in P. aeruginosa. Through an extensive screening of natural compounds from diverse sources, we identified Juglone, a natural compound from walnut, as a promising candidate. We showed that Juglone could inhibit PqsR and the molecular docking results revealed that Juglone could potentially bind to the PqsR active site. Furthermore, Juglone could inhibit pqs-regulated virulence factors, such as pyocyanin and the PQS QS signaling molecule. Juglone could also significantly reduce both the quantity and quality of P. aeruginosa biofilms. Notably, this compound exhibited minimal cytotoxicity toward mammalian cells, suggesting its potential safety for therapeutic applications. To explore the clinical relevance of Juglone, we investigated its combinatorial effects with colistin, a commonly used antibiotic against P. aeruginosa infections. The Juglone-colistin combinatorial treatment could eliminate biofilms formed by wild-type P. aeruginosa PAO1 and its clinical isolates collected from cystic fibrosis patients. The Juglone-colistin combinatorial therapy dramatically improved colistin efficacy and reduced inflammation in a wound infection model, indicating its potential for clinical utility. In conclusion, the discovery of Juglone provides insights into the development of innovative antivirulence therapeutic strategies to combat P. aeruginosa biofilm-associated infections.
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Affiliation(s)
- Yeping Ma
- Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
| | - Wing Suet Tang
- Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
| | - Sylvia Yang Liu
- Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
| | - Bee Luan Khoo
- Department
of Biomedical Engineering, City University
of Hong Kong, Kowloon, Hong Kong SAR 999077, China
- Hong
Kong Center for Cerebro-Cardiovascular Health Engineering (COCHE), Hong Kong SAR 999077, China
- City
University of Hong Kong–Shenzhen Futian Research Institute, Shenzhen 518172, China
| | - Song Lin Chua
- Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
- State
Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
- Research
Centre of Deep Space Explorations (RCDSE), The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
- Research
Institute for Future Food (RiFood), The
Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
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16
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Kovács M, Wojnárovits L, Homlok R, Tegze A, Mohácsi-Farkas C, Takács E, Belák Á. Changes in the behavior of Staphylococcus aureus strains in the presence of oxacillin under the effect of gamma radiation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122843. [PMID: 37918768 DOI: 10.1016/j.envpol.2023.122843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Staphylococcus aureus (S. aureus) as a major pathogen is implicated in a wide range of foodborne and hospital-acquired infections, its methicillin resistant variants contribute to the spread of β-lactam antibiotic resistance. It is essentially important to destroy these pathogens, their resistance genes and the antibiotics in wastewaters. For this purpose reactions of reactive radicals (advanced oxidation processes), first of all hydroxyl radicals (•OH), are suggested. Here the radiolysis of water supplied these radicals. In the experiments B.01755 oxacillin sensitive and B.02174 resistant S. aureus strains were used to study their behaviorr in suspensions under the effect of irradiation in presence and absence of oxacillin. Oxacillin inactivation depended on concentration of the antibiotic used (0.042 and 1 g dm-3), higher concentration required a higher dose. When 106-109 CFU cm-3 S. aureus suspensions were irradiated with γ-radiation the bacteria were inactivated at low absorbed doses: 4 orders of magnitude decrease ocurred in the number of culturable cells at ∼0.6 kGy dose. Both cell membrane and DNA suffered considerable damages during irradiation. Due to the membrane damage the cells could not be stained, and the DNA content of cells in several days period was released into the solution. In DNA damage the oxacillin resistance mecA gene was also modified, it did not multiply in PCR test. These findings are important from the point of view of applying irradiation technology to stop the spread of antibiotic resistance.
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Affiliation(s)
- Mónika Kovács
- Department of Food Microbiology, Hygiene and Safety, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, H-1118, Budapest, Somlói út 14-16, Hungary.
| | - László Wojnárovits
- Radiation Chemistry Department, Institute for Energy Security and Environmental Safety, Centre for Energy Research, H-1121, Budapest, Konkoly-Thege Miklós út 29-33, Hungary.
| | - Renáta Homlok
- Radiation Chemistry Department, Institute for Energy Security and Environmental Safety, Centre for Energy Research, H-1121, Budapest, Konkoly-Thege Miklós út 29-33, Hungary.
| | - Anna Tegze
- Radiation Chemistry Department, Institute for Energy Security and Environmental Safety, Centre for Energy Research, H-1121, Budapest, Konkoly-Thege Miklós út 29-33, Hungary.
| | - Csilla Mohácsi-Farkas
- Department of Food Microbiology, Hygiene and Safety, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, H-1118, Budapest, Somlói út 14-16, Hungary.
| | - Erzsébet Takács
- Radiation Chemistry Department, Institute for Energy Security and Environmental Safety, Centre for Energy Research, H-1121, Budapest, Konkoly-Thege Miklós út 29-33, Hungary.
| | - Ágnes Belák
- Department of Food Microbiology, Hygiene and Safety, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, H-1118, Budapest, Somlói út 14-16, Hungary.
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17
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Yaghmoor RB, Abdel-Hadi M, Petridis H, Allan E, Young AM. Effects of Novel Dental Composites on Streptococcus mutans Biofilms. J Funct Biomater 2023; 15:13. [PMID: 38248680 PMCID: PMC10817267 DOI: 10.3390/jfb15010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024] Open
Abstract
With the phase-out of amalgam and the increase in minimally invasive dentistry, there is a growing need for high-strength composite materials that can kill residual bacteria and promote tooth remineralization. This study quantifies how antibacterial polylysine (PLS) and re-mineralizing monocalcium phosphate monohydrate (MCPM) affect Streptococcus mutans biofilms and the strength of dental composites. For antibacterial studies, the MCPM-PLS filler percentages were 0-0, 8-4, 12-6, and 16-8 wt% of the composite filler phase. Composite discs were immersed in 0.1% sucrose-supplemented broth containing Streptococcus mutans (UA159) and incubated in an anaerobic chamber for 48 h. Surface biomass was determined by crystal violet (CV) staining. Growth medium pH was measured at 24 and 48 h. Biofilm bacterial viability (CFU), exo-polysaccharide (water-soluble glucan (WSG) and water-insoluble glucan (WIG)), and extracellular DNA (eDNA) were quantified. This was by serial dilution plate counting, phenol-sulfuric acid microassay, and fluorometry, respectively. The biaxial flexural strengths were determined after water immersion for 1 week, 1 month, and 1 year. The MCPM-PLS wt% were 8-4, 8-8, 16-4 and 16-8. The normalized biomass, WSG, and WIG showed a linear decline of 66%, 64%, and 55%, respectively, as the PLS level increased up to 8%. The surrounding media pH (4.6) was all similar. A decrease in bacterial numbers with the 12-6 formula and a significant reduction with 16-8 compared to the 0-0 formulation was observed. The eDNA concentrations in biofilms formed on 12-6 and 16-8 formulations were significantly less than the 0-0 control and 8-4 formulations. Doubling MCPM and PLS caused a 14 and 19% reduction in strength in 1 week, respectively. Average results were lower at 1 month and 1 year but affected less upon doubling MCPM and PLS levels. Moreover, a 4% PLS may help to reduce total biomass and glucan levels in biofilms on the above composites. Higher levels are required to reduce eDNA and provide bactericidal action, but these can decrease early strength.
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Affiliation(s)
- Rayan B. Yaghmoor
- Department of Restorative Dentistry, College of Dental Medicine, Umm Al-Qura University, Makkah 24381, Saudi Arabia;
| | - Mohammad Abdel-Hadi
- Unit of Prosthodontics, Department of Restorative Dentistry, UCL Eastman Dental Institute, Rockefeller Building, London WC1E 6HX, UK; (M.A.-H.); (H.P.)
| | - Haralampos Petridis
- Unit of Prosthodontics, Department of Restorative Dentistry, UCL Eastman Dental Institute, Rockefeller Building, London WC1E 6HX, UK; (M.A.-H.); (H.P.)
| | - Elaine Allan
- Department of Microbial Diseases, UCL Eastman Dental Institute, Royal Free Hospital, London NW3 2QG, UK;
| | - Anne M. Young
- Department of Biomaterials and Tissue Engineering, UCL Eastman Dental Institute, Royal Free Hospital, London NW3 2QG, UK
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18
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Heredia-Ponce Z, Secchi E, Toyofuku M, Marinova G, Savorana G, Eberl L. Genotoxic stress stimulates eDNA release via explosive cell lysis and thereby promotes streamer formation of Burkholderia cenocepacia H111 cultured in a microfluidic device. NPJ Biofilms Microbiomes 2023; 9:96. [PMID: 38071361 PMCID: PMC10710452 DOI: 10.1038/s41522-023-00464-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
DNA is a component of biofilms, but the triggers of DNA release during biofilm formation and how DNA contributes to biofilm development are poorly investigated. One key mechanism involved in DNA release is explosive cell lysis, which is a consequence of prophage induction. In this article, the role of explosive cell lysis in biofilm formation was investigated in the opportunistic human pathogen Burkholderia cenocepacia H111 (H111). Biofilm streamers, flow-suspended biofilm filaments, were used as a biofilm model in this study, as DNA is an essential component of their matrix. H111 contains three prophages on chromosome 1 of its genome, and the involvement of each prophage in causing explosive cell lysis of the host and subsequent DNA and membrane vesicle (MV) release, as well as their contribution to streamer formation, were studied in the presence and absence of genotoxic stress. The results show that two of the three prophages of H111 encode functional lytic prophages that can be induced by genotoxic stress and their activation causes DNA and MVs release by explosive cell lysis. Furthermore, it is shown that the released DNA enables the strain to develop biofilm streamers, and streamer formation can be enhanced by genotoxic stress. Overall, this study demonstrates the involvement of prophages in streamer formation and uncovers an often-overlooked problem with the use of antibiotics that trigger the bacterial SOS response for the treatment of bacterial infections.
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Affiliation(s)
- Zaira Heredia-Ponce
- Department of Plant and Microbial Biology, University of Zürich, 8008, Zürich, Switzerland
| | - Eleonora Secchi
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093, Zürich, Switzerland
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Gabriela Marinova
- Department of Plant and Microbial Biology, University of Zürich, 8008, Zürich, Switzerland
| | - Giovanni Savorana
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093, Zürich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, 8008, Zürich, Switzerland.
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19
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de Alteriis E, Incerti G, Cartenì F, Chiusano ML, Colantuono C, Palomba E, Termolino P, Monticolo F, Esposito A, Bonanomi G, Capparelli R, Iannaccone M, Foscari A, Landi C, Parascandola P, Sanchez M, Tirelli V, de Falco B, Lanzotti V, Mazzoleni S. Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:292-295. [PMID: 38053574 PMCID: PMC10695634 DOI: 10.15698/mic2023.12.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.
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Affiliation(s)
- Elisabetta de Alteriis
- Department of Biology, University of Naples “Federico II”, Via Cinthia 26, 80126 Naples, Italy
| | - Guido Incerti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Fabrizio Cartenì
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Emanuela Palomba
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici (NA), Italy
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici (NA), Italy
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Alfonso Esposito
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Task Force Microbiome - University of Naples “Federico II“
| | - Rosanna Capparelli
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Marco Iannaccone
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Laboratory of Biotechnological Processes for Energy and Industry, ENEA, Via Anguillarese, 301, - 00123 Rome, Italy
| | - Alessandro Foscari
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Carmine Landi
- Department of Industrial Engineering, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy-
| | - Palma Parascandola
- Department of Industrial Engineering, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy-
| | - Massimo Sanchez
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy
| | - Valentina Tirelli
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy
| | - Bruna de Falco
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Virginia Lanzotti
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Task Force Microbiome - University of Naples “Federico II“
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20
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Wang Z, Gao J, Zhao Y, Guo Y, Zhang Y, Yuan Y, Zhao M, Zeng L. Fates of extracellular and intracellular antibiotic resistance genes in activated sludge and plastisphere under sulfadiazine pressure. WATER RESEARCH 2023; 247:120752. [PMID: 37898001 DOI: 10.1016/j.watres.2023.120752] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023]
Abstract
Microplastics, antibiotics, and antibiotic resistance genes (ARGs) represent prominent emerging contaminants that can potentially hinder the efficacy of biological wastewater treatment and pose health risks. Plastisphere as a distinct ecological niche for microorganisms, acts as a repository for ARGs and potential pathogenic bacteria. Nonetheless, the spread pattern of extracellular ARGs (eARGs) and intracellular ARGs (iARGs) in plastisphere under antibiotic exposure was not yet known. This study aimed to investigate disparities in extracellular polymeric substances (EPS) production, extracellular and intracellular microbial community structures, as well as the transmission of eARGs and iARGs between activated sludge and plastisphere in an anaerobic/anoxic/oxic system under sulfadiazine (SDZ) exposure. SDZ was found to enhance EPS production in activated sludge and plastisphere. Interestingly, as SDZ removal efficiency increased, EPS content decreased in activated sludge and plastisphere collected from oxic zone, and continued to increase in plastisphere samples collected from anaerobic and anoxic zones. There were significant differences in microbial community structure between activated sludge and plastisphere, and the DNA fragments of potential pathogenic bacteria were detected in extracellular samples. SDZ exhibited a promoting effect on the propagation of eARGs, which were more abundant in the plastisphere than in activated sludge, thus heightening the risk of ARGs dissemination. Extracellular mobile genetic elements played a pivotal role in driving the spread of eARGs, while the microbial community induced the changes of iARGs. Potential pathogenic bacteria emerged as potential hosts for ARGs and mobile genetic elements within activated sludge and plastisphere, leading to more serious environmental threats.
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Affiliation(s)
- Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Yifan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Guo
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yukun Yuan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Mingyan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Liqin Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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21
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Zhou X, Wells MJ, Gordon VD. Incorporation of collagen into Pseudomonas aeruginosa and Staphylococcus aureus biofilms impedes phagocytosis by neutrophils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564018. [PMID: 37961328 PMCID: PMC10634824 DOI: 10.1101/2023.10.25.564018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Biofilms are communities of microbes embedded in a matrix of extracellular polymeric substances (EPS). Matrix components can be produced by biofilm organisms and can also originate from the environment and then be incorporated into the biofilm. For example, we have recently shown that collagen, a host-produced protein that is abundant in many different infection sites, can be taken up into the biofilm matrix, altering biofilm mechanics. The biofilm matrix protects bacteria from clearance by the immune system, and some of that protection likely arises from the mechanical properties of the biofilm. Pseudomonas aeruginosa and Staphylococcus aureus are common human pathogens notable for forming biofilm infections in anatomical sites rich in collagen. Here, we show that the incorporation of Type I collagen into P. aeruginosa and S. aureus biofilms significantly hinders phagocytosis of biofilm bacteria by human neutrophils. However, enzymatic treatment with collagenase, which breaks down collagen, can partly or entirely negate the protective effect of collagen and restore the ability of neutrophils to engulf biofilm bacteria. From these findings, we suggest that enzymatic degradation of host materials may be a potential way to compromise biofilm infections and enhance the efficacy of the host immune response without promoting antibiotic resistance. Such an approach might be beneficial both in cases where the infecting species is known and also in cases wherein biofilm components are not readily known, such as multispecies infections or infections by unknown species.
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Affiliation(s)
- Xuening Zhou
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
- Interdisciplinary Life Sciences Graduate Program, Norman Hackerman Building, 100 East 24th St., NHB 4500, Austin, Texas 78712, USA
| | - Marilyn J Wells
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
| | - Vernita D Gordon
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
- Interdisciplinary Life Sciences Graduate Program, Norman Hackerman Building, 100 East 24th St., NHB 4500, Austin, Texas 78712, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Neural Molecular Science Building, 2506 Speedway, Stop A5000, Austin, Texas 78712, USA
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22
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Guadarrama-Orozco KD, Perez-Gonzalez C, Kota K, Cocotl-Yañez M, Jiménez-Cortés JG, Díaz-Guerrero M, Hernández-Garnica M, Munson J, Cadet F, López-Jácome LE, Estrada-Velasco ÁY, Fernández-Presas AM, García-Contreras R. To cheat or not to cheat: cheatable and non-cheatable virulence factors in Pseudomonas aeruginosa. FEMS Microbiol Ecol 2023; 99:fiad128. [PMID: 37827541 DOI: 10.1093/femsec/fiad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023] Open
Abstract
Important bacterial pathogens such as Pseudomonas aeruginosa produce several exoproducts such as siderophores, degradative enzymes, biosurfactants, and exopolysaccharides that are used extracellularly, benefiting all members of the population, hence being public goods. Since the production of public goods is a cooperative trait, it is in principle susceptible to cheating by individuals in the population who do not invest in their production, but use their benefits, hence increasing their fitness at the expense of the cooperators' fitness. Among the most studied virulence factors susceptible to cheating are siderophores and exoproteases, with several studies in vitro and some in animal infection models. In addition to these two well-known examples, cheating with other virulence factors such as exopolysaccharides, biosurfactants, eDNA production, secretion systems, and biofilm formation has also been studied. In this review, we discuss the evidence of the susceptibility of each of those virulence factors to cheating, as well as the mechanisms that counteract this behavior and the possible consequences for bacterial virulence.
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Affiliation(s)
- Katya Dafne Guadarrama-Orozco
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Caleb Perez-Gonzalez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Kokila Kota
- Ramapo College of New Jersey, Biology Department, Mahwah, NJ 07430, USA
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Jesús Guillermo Jiménez-Cortés
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Miguel Díaz-Guerrero
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Mariel Hernández-Garnica
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Julia Munson
- Ramapo College of New Jersey, Biology Department, Mahwah, NJ 07430, USA
| | - Frederic Cadet
- PEACCEL, Artificial Intelligence Department, AI for Biologics, Paris, 75013, France
| | - Luis Esaú López-Jácome
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389 Mexico City, Mexico
| | - Ángel Yahir Estrada-Velasco
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Ana María Fernández-Presas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
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23
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Kalia VC, Patel SKS, Lee JK. Bacterial biofilm inhibitors: An overview. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115389. [PMID: 37634478 DOI: 10.1016/j.ecoenv.2023.115389] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/05/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
Bacteria that cause infectious diseases adopt biofilms as one of their most prevalent lifestyles. Biofilms enable bacteria to tolerate environmental stress and evade antibacterial agents. This bacterial defense mechanism has rendered the use of antibiotics ineffective for the treatment of infectious diseases. However, many highly drug-resistant microbes have rapidly emerged owing to such treatments. Different signaling mechanisms regulate bacterial biofilm formation, including cyclic dinucleotide (c-di-GMP), small non-coding RNAs, and quorum sensing (QS). A cell density-dependent phenomenon, QS is associated with c-di-GMP (a global messenger), which regulates gene expression related to adhesion, extracellular matrix production, the transition from the planktonic to biofilm stage, stability, pathogenicity, virulence, and acquisition of nutrients. The article aims to provide information on inhibiting biofilm formation and disintegrating mature/preformed biofilms. This treatment enables antimicrobials to target the free-living/exposed bacterial cells at lower concentrations than those needed to treat bacteria within the biofilm. Therefore, a complementary action of antibiofilm and antimicrobial agents can be a robust strategic approach to dealing with infectious diseases. Taken together, these molecules have broad implications for human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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24
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Xue Y, Abdullah Al M, Chen H, Xiao P, Zhang H, Jeppesen E, Yang J. Relic DNA obscures DNA-based profiling of multiple microbial taxonomic groups in a river-reservoir ecosystem. Mol Ecol 2023; 32:4940-4952. [PMID: 37452629 DOI: 10.1111/mec.17071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Numerous studies have investigated the spatiotemporal variability in water microbial communities, yet the effects of relic DNA on microbial community profiles, especially microeukaryotes, remain far from fully understood. Here, total and active bacterial and microeukaryotic community compositions were characterized using propidium monoazide (PMA) treatment coupled with high-throughput sequencing in a river-reservoir ecosystem. Beta diversity analysis showed a significant difference in community composition between both the PMA untreated and treated bacteria and microeukaryotes; however, the differentiating effect was much stronger for microeukaryotes. Relic DNA only resulted in underestimation of the relative abundances of Bacteroidota and Nitrospirota, while other bacterial taxa exhibited no significant changes. As for microeukaryotes, the relative abundances of some phytoplankton (e.g. Chlorophyta, Dinoflagellata and Ochrophyta) and fungi were greater after relic DNA removal, whereas Cercozoa and Ciliophora showed the opposite trend. Moreover, relic DNA removal weakened the size and complexity of cross-trophic microbial networks and significantly changed the relationships between environmental factors and microeukaryotic community composition. However, there was no significant difference in the rates of temporal community turnover between the PMA untreated and treated samples for either bacteria or microeukaryotes. Overall, our results imply that the presence of relic DNA in waters can give misleading information of the active microbial community composition, co-occurrence networks and their relationships with environmental conditions. More studies of the abundance, decay rate and functioning of nonviable DNA in freshwater ecosystems are highly recommended in the future.
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Affiliation(s)
- Yuanyuan Xue
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Huihuang Chen
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xiao
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Hongteng Zhang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Erik Jeppesen
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Sino-Danish Centre for Education and Research, Beijing, China
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Turkey
- Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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25
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Saengrung J, Bunnoy A, Du X, Huang L, An R, Liang X, Srisapoome P. Effects of ribonucleotide supplementation in modulating the growth of probiotic Bacillus subtilis and the synergistic benefits for improving the health performance of Asian seabass (Lates calcarifer). FISH & SHELLFISH IMMUNOLOGY 2023; 140:108983. [PMID: 37541637 DOI: 10.1016/j.fsi.2023.108983] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/03/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
In aquaculture, due to the requirements for high-density culture, the diseases caused by bacterial pathogens have become a serious issue. To solve this problem, we performed synbiotic application of RNA and Bacillus subtilis as a sustainable and eco-friendly approach to improve the health and immunity of Asian seabass (Lates calcarifer) during cultivation without using any harmful antibiotics or chemicals. Among various forms of nucleic acids, such as mononucleotides and DNA, RNA was found to be most effective in promoting the growth performance of probiotic B. subtilis in all the tested minimal medium conditions. Accordingly, we used the synbiotic combination of B. subtilis and RNA for Asian seabass cultivation. After feed supplementation for fourteen days, the fish that received the combination treatment exhibited a significant increase in innate cellular and humoral immune parameters, including phagocytic activity, phagocytic index, respiratory burst, serum lysozyme and bactericidal activities, as well as upregulated expression of immune-related genes, including HEPC1, A2M, C3, CC, CLEC, LYS, HSP70, and HSP90. Furthermore, significant increases were observed in the ileal villus height and goblet cell numbers in the intestinal villi in all fish treatment groups. The combination treatment did not cause histopathological abnormalities in the intestine and liver, suggesting that the synbiotic treatment is safe for use in fish. The treated Asian seabass also exhibited a significantly increased survival rate after Aeromonas hydrophila challenge. These results indicate that the synbiotic mixture of B. subtilis and RNA can be considered a beneficial feed additive and immunostimulant for Asian seabass cultivation.
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Affiliation(s)
- Jureerat Saengrung
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China; Center of Excellence in Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, 10900, Bangkok, Thailand; Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, 10900, Bangkok, Thailand.
| | - Anurak Bunnoy
- Center of Excellence in Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, 10900, Bangkok, Thailand; Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, 10900, Bangkok, Thailand.
| | - Xinmei Du
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Lili Huang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Prapansak Srisapoome
- Center of Excellence in Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, 10900, Bangkok, Thailand; Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, 10900, Bangkok, Thailand.
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26
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Garg SS, Dubey R, Sharma S, Vyas A, Gupta J. Biological macromolecules-based nanoformulation in improving wound healing and bacterial biofilm-associated infection: A review. Int J Biol Macromol 2023; 247:125636. [PMID: 37392924 DOI: 10.1016/j.ijbiomac.2023.125636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
A chronic wound is a serious complication associated with diabetes mellitus and is difficult to heal due to high glucose levels, oxidative stress, and biofilm-associated microbial infection. The structural complexity of microbial biofilm makes it impossible for antibiotics to penetrate the matrix, hence conventional antibiotic therapies became ineffective in clinical settings. This demonstrates an urgent need to find safer alternatives to reduce the prevalence of chronic wound infection associated with microbial biofilm. A novel approach to address these concerns is to inhibit biofilm formation using biological-macromolecule based nano-delivery system. Higher drug loading efficiency, sustained drug release, enhanced drug stability, and improved bioavailability are advantages of employing nano-drug delivery systems to prevent microbial colonization and biofilm formation in chronic wounds. This review covers the pathogenesis, microbial biofilm formation, and immune response to chronic wounds. Furthermore, we also focus on macromolecule-based nanoparticles as wound healing therapies to reduce the increased mortality associated with chronic wound infections.
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Affiliation(s)
- Sourbh Suren Garg
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Rupal Dubey
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Lovely Professional University, Punjab, India
| | - Sandeep Sharma
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Lovely Professional University, Punjab, India
| | - Ashish Vyas
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Jeena Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India.
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27
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Dicks LMT. Biofilm Formation of Clostridioides difficile, Toxin Production and Alternatives to Conventional Antibiotics in the Treatment of CDI. Microorganisms 2023; 11:2161. [PMID: 37764005 PMCID: PMC10534356 DOI: 10.3390/microorganisms11092161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile is considered a nosocomial pathogen that flares up in patients exposed to antibiotic treatment. However, four out of ten patients diagnosed with C. difficile infection (CDI) acquired the infection from non-hospitalized individuals, many of whom have not been treated with antibiotics. Treatment of recurrent CDI (rCDI) with antibiotics, especially vancomycin (VAN) and metronidazole (MNZ), increases the risk of experiencing a relapse by as much as 70%. Fidaxomicin, on the other hand, proved more effective than VAN and MNZ by preventing the initial transcription of RNA toxin genes. Alternative forms of treatment include quorum quenching (QQ) that blocks toxin synthesis, binding of small anion molecules such as tolevamer to toxins, monoclonal antibodies, such as bezlotoxumab and actoxumab, bacteriophage therapy, probiotics, and fecal microbial transplants (FMTs). This review summarizes factors that affect the colonization of C. difficile and the pathogenicity of toxins TcdA and TcdB. The different approaches experimented with in the destruction of C. difficile and treatment of CDI are evaluated.
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Affiliation(s)
- Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
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28
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Chauhan C, Kaundal RK. Understanding the role of cGAS-STING signaling in ischemic stroke: a new avenue for drug discovery. Expert Opin Drug Discov 2023; 18:1133-1149. [PMID: 37537969 DOI: 10.1080/17460441.2023.2244409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
INTRODUCTION Ischemic stroke is a significant global health challenge with limited treatment options. Neuroinflammation, driven by microglial activation, plays a critical role in stroke pathophysiology. The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway has emerged as a key player in microglial activation, sterile neuroinflammation, and cell death following stroke. Understanding the interplay between this pathway and stroke pathophysiology is crucial for exploring newer therapeutics for stroke patients. AREAS COVERED This review discusses the pivotal role of the cGAS-STING pathway in ischemic stroke. It explores the interplay between cGAS-STING activation, neuroinflammation, microglia activation, M2 polarization, neutrophil infiltration, and cytokine release. Additionally, the authors examine its contributions to various cell death programs (pyroptosis, apoptosis, necroptosis, lysosomal cell death, autophagy, and ferroptosis). The review summarizes recent studies on targeting cGAS-STING signaling in stroke, highlighting the therapeutic potential of small molecule inhibitors and RNA-based approaches in mitigating neuroinflammation, preventing cell death, and improving patient outcomes. EXPERT OPINION Understanding cGAS-STING signaling in ischemic stroke offers an exciting avenue for drug discovery. Targeting this pathway holds promise for developing novel therapeutics that effectively mitigate neuroinflammation, prevent cell death, and enhance patient outcomes. Further research and development of therapeutic strategies are warranted to fully exploit the potential of this pathway as a therapeutic target for stroke.
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Affiliation(s)
- Chandan Chauhan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Lucknow, India
| | - Ravinder Kumar Kaundal
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Lucknow, India
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29
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Extracellular matrix affects mature biofilm and stress resistance of psychrotrophic spoilage Pseudomonas at cold temperature. Food Microbiol 2023; 112:104214. [PMID: 36906314 DOI: 10.1016/j.fm.2023.104214] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/08/2023]
Abstract
Psychrotrophic Pseudomonas as the dominant spoilage bacteria, have biofilm forming ability, increasing persistence and contamination in the chilled food. Biofilm formation of spoilage Pseudomonas at cold temperature was documented, however, role of extracellular matrix in mature biofilm and stress resistance of psychrotrophic Pseudomonas are much less abundant. The aim of this study was to investigate the biofilm forming characteristics of three spoilers P. fluorescens PF07, P. lundensis PL28, and P. psychrophile PP26 at 25 °C, 15 °C and 4 °C, and to explore their stress resistance to chemical and thermal treatments of mature biofilms. The results showed that biofilm biomass of three Pseudomonas at 4 °C was significantly higher than that at 15 °C and 25 °C. The secretion of extracellular polymeric substances (EPS) greatly increased in those Pseudomonas under low temperature, of which extracellular protein constituted about 71.03%-77.44%. Compared to 25 °C, the mature biofilms were observed to more aggregation and thicker spatial structure at 4 °C ranging from 42.7 to 54.6 μm, in contrast to 25.0-29.8 μm at 25 °C, especially strain PF07. These Pseudomonas biofilms switched into moderate hydrophobicity, and their swarming and swimming were significantly inhibited at low temperature. Furthermore, the resistance to NaClO and heating at 65 °C apparently enhanced for mature biofilm formed at 4 °C, indicating the difference in EPS matrix production influenced the stress resistance of biofilm. In addition, three strains contained alg and psl operons for exopolysaccharide biosynthesis, and biofilm related genes of algK, pslA, rpoS, and luxR were significantly up-regulated, while flgA gene was down-regulated at 4 °C compared to 25 °C, consistent with the above phenotype changes. Thus, the dramatic increase of mature biofilm and their stress resistance in psychrotrophic Pseudomonas were associated with large secretion and protection of extracellular matrix under low temperature, which provide a theoretical basis for subsequent biofilm control during cold chain.
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30
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Medina Caro D, Horstmann L, Ganzert L, Oses R, Friedl T, Wagner D. An improved method for intracellular DNA (iDNA) recovery from terrestrial environments. Microbiologyopen 2023; 12:e1369. [PMID: 37379428 DOI: 10.1002/mbo3.1369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023] Open
Abstract
The simultaneous extraction of intracellular DNA (iDNA) and extracellular DNA (eDNA) can help to separate the living in situ community (represented by iDNA) from background DNA that originated both from past communities and from allochthonous sources. As iDNA and eDNA extraction protocols require separating cells from the sample matrix, their DNA yields are generally lower than direct methods that lyse the cells within the sample matrix. We, therefore, tested different buffers with and without adding a detergent mix (DM) in the extraction protocol to improve the recovery of iDNA from surface and subsurface samples that covered a variety of terrestrial environments. The combination of a highly concentrated sodium phosphate buffer plus DM significantly improved iDNA recovery for almost all tested samples. Additionally, the combination of sodium phosphate and EDTA improved iDNA recovery in most of the samples and even allowed the successful extraction of iDNA from extremely low-biomass iron-bearing rock samples taken from the deep biosphere. Based on our results, we recommend using a protocol with sodium phosphate in combination with either a DM (NaP 300 mM + DM) or EDTA (NaP + EDTA 300 mM). Furthermore, for studies that rely on the eDNA pool, we recommend using buffers solely based on sodium phosphate because the addition of EDTA or a DM resulted in a decrease in eDNA for most of the tested samples. These improvements can help reduce community bias in environmental studies and contribute to better characterizations of both modern and past ecosystems.
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Affiliation(s)
- Diego Medina Caro
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Lucas Horstmann
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Department Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University Göttingen, Göttingen, Germany
| | - Lars Ganzert
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Marbio, UiT The Arctic University of Norway, Tromsø, Norway
| | - Romulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copiapó, Chile
| | - Thomas Friedl
- Department Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University Göttingen, Göttingen, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
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31
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Sun YQ, Ge Y. Relic DNA effects on the estimates of bacterial community composition and taxa dynamics in soil. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12576-3. [PMID: 37191685 DOI: 10.1007/s00253-023-12576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/07/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
DNA-based analyses have become routine methods in soil microbial research, for their high throughput and resolution in characterizing microbial communities. Yet, concerns arise regarding the interference of relic DNA in estimates of viable bacterial community composition and individual taxa dynamics in soils that recovered from post-gamma irradiation. In this study, different soil samples with varying bacterial diversity but similar soil properties were randomly selected. We split each sample into two parts: one part was treated with propidium monoazide (PMA) before DNA extraction, PMA can bind to relic DNA and inhibit PCR amplification by chemical modification; DNA of the other part was extracted following the same process but without PMA pretreatment. Then, soil bacterial abundance was quantified by quantitative polymerase chain reaction, and bacterial community structure was examined by Illumina metabarcoding sequencing of 16S rRNA gene. The results showed that the higher bacterial richness and evenness were estimated when relic DNA was present. The variation trends of bacterial abundance, alpha diversity, and beta diversity remained the same, as reflected by the significant correlations between PMA-treated and -untreated samples (P < 0.05). Moreover, as the mean abundance increased, the reproducibility of detecting individual taxa dynamics between relic DNA present and absent treatments increased. These findings provide empirical evidence that a more even distribution of species abundance derived from relic DNA would result in the overestimation of richness in the total DNA pools and also have crucial implications for guiding proper application of high-throughput sequencing to estimate bacterial community diversity and taxonomic population dynamic. KEY POINTS: • Relic DNA effects on the bacterial community in sterilized soils were assessed. • More even species abundance distribution in relic DNA overestimates true richness. • The reproducibility of individual taxa dynamics increased with their abundance.
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Affiliation(s)
- Yao-Qin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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32
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Sivalingam P, Sabatino R, Sbaffi T, Fontaneto D, Corno G, Di Cesare A. Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121325. [PMID: 36828358 DOI: 10.1016/j.envpol.2023.121325] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/04/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.
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Affiliation(s)
- Periyasamy Sivalingam
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Tomasa Sbaffi
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Diego Fontaneto
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Gianluca Corno
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy.
| | - Andrea Di Cesare
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
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Villa F, Ludwig N, Mazzini S, Scaglioni L, Fuchs AL, Tripet B, Copié V, Stewart PS, Cappitelli F. A desiccated dual-species subaerial biofilm reprograms its metabolism and affects water dynamics in limestone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161666. [PMID: 36669662 DOI: 10.1016/j.scitotenv.2023.161666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Understanding the impact of sessile communities on underlying materials is of paramount importance in stone conservation. Up until now, the critical role of subaerial biofilms (SABs) whether they are protective or deteriorative remains unclear, especially under desiccation. The interest in desiccated SABs is raised by the prediction of an increase in drought events in the next decades that will affect the Mediterranean regions' rich stone heritage as never before. Thus, the main goal of this research is to study the effects of desiccation on both the biofilms' eco-physiology and its impacts on the lithic substrate. To this end, we used a dual-species model system composed of a phototroph and a chemotroph to simulate biofilm behavior on stone heritage. We found that drought altered the phototroph-chemotroph balance and enriched the biofilm matrix with proteins and DNA. Desiccated SABs underwent a shift in metabolism to fermentation and a decrease in oxidative stress. Additionally, desiccated SABs changed the water-related dynamics (adsorption, evaporation, and wetting properties) in limestone. Water absorption experiments showed that desiccated SABs protected the stone from rapid water uptake, while a thermographic survey indicated a delay in water evaporation. Spilling-drop tests revealed a change in the wettability of the stone-SAB interface, which affected the water transport properties of the stone. Finally, desiccated SABs reduced stone swelling in the presence of water vapor. The biodeteriorative and bioprotective implications of desiccated SABs on the stone were ultimately assessed.
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Affiliation(s)
- F Villa
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - N Ludwig
- Dipartimento di Fisica Aldo Pontremoli, Università degli Studi di Milano, 20133 Milan, Italy.
| | - S Mazzini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - L Scaglioni
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - A L Fuchs
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, USA
| | - B Tripet
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, USA.
| | - V Copié
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, USA.
| | - P S Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman 59717, USA.
| | - F Cappitelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
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Cheng YY, Chen Z, Cao X, Ross TD, Falbel TG, Burton BM, Venturelli OS. Programming bacteria for multiplexed DNA detection. Nat Commun 2023; 14:2001. [PMID: 37037805 PMCID: PMC10086068 DOI: 10.1038/s41467-023-37582-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023] Open
Abstract
DNA is a universal and programmable signal of living organisms. Here we develop cell-based DNA sensors by engineering the naturally competent bacterium Bacillus subtilis (B. subtilis) to detect specific DNA sequences in the environment. The DNA sensor strains can identify diverse bacterial species including major human pathogens with high specificity. Multiplexed detection of genomic DNA from different species in complex samples can be achieved by coupling the sensing mechanism to orthogonal fluorescent reporters. We also demonstrate that the DNA sensors can detect the presence of species in the complex samples without requiring DNA extraction. The modularity of the living cell-based DNA-sensing mechanism and simple detection procedure could enable programmable DNA sensing for a wide range of applications.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhengyi Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler D Ross
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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35
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Cheng YY, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM, Venturelli OS. Efficient plasmid transfer via natural competence in a microbial co-culture. Mol Syst Biol 2023; 19:e11406. [PMID: 36714980 PMCID: PMC9996237 DOI: 10.15252/msb.202211406] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - James M Papadopoulos
- Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Jason D Zuke
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin, Madison, WI, USA.,Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
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36
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Dong J, Liu L, Chen L, Xiang Y, Wang Y, Zhao Y. The Coexistence of Bacterial Species Restructures Biofilm Architecture and Increases Tolerance to Antimicrobial Agents. Microbiol Spectr 2023; 11:e0358122. [PMID: 36847543 PMCID: PMC10100793 DOI: 10.1128/spectrum.03581-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Chronic infections caused by polymicrobial biofilms are often difficult to treat effectively, partially due to the elevated tolerance of polymicrobial biofilms to antimicrobial treatments. It is known that interspecific interactions influence polymicrobial biofilm formation. However, the underlying role of the coexistence of bacterial species in polymicrobial biofilm formation is not fully understood. Here, we investigated the effect of the coexistence of Enterococcus faecalis, Escherichia coli O157:H7, and Salmonella enteritidis on triple-species biofilm formation. Our results demonstrated that the coexistence of these three species enhanced the biofilm biomass and led to restructuring of the biofilm into a tower-like architecture. Furthermore, the proportions of polysaccharides, proteins, and eDNAs in the extracellular matrix (ECM) composition of the triple-species biofilm were significantly changed compared to those in the E. faecalis mono-species biofilm. Finally, we analyzed the transcriptomic profile of E. faecalis in response to coexistence with E. coli and S. enteritidis in the triple-species biofilm. The results suggested that E. faecalis established dominance and restructured the triple-species biofilm by enhancing nutrient transport and biosynthesis of amino acids, upregulating central carbon metabolism, manipulating the microenvironment through "biological weapons," and activating versatile stress response regulators. Together, the results of this pilot study reveal the nature of E. faecalis-harboring triple-species biofilms with a static biofilm model and provide novel insights for further understanding interspecies interactions and the clinical treatment of polymicrobial biofilms. IMPORTANCE Bacterial biofilms possess distinct community properties that affect various aspects of our daily lives. In particular, biofilms exhibit increased tolerance to chemical disinfectants, antimicrobial agents, and host immune responses. Multispecies biofilms are undoubtedly the dominant form of biofilms in nature. Thus, there is a pressing need for more research directed at delineating the nature of multispecies biofilms and the effects of the properties on the development and survival of the biofilm community. Here, we address the effects of the coexistence of Enterococcus faecalis, Escherichia coli, and Salmonella enteritidis on triple-species biofilm formation with a static model. In combination with transcriptomic analyses, this pilot study explores the potential underlying mechanisms that lead to the dominance of E. faecalis in triple-species biofilms. Our findings provide novel insights into the nature of triple-species biofilms and indicate that the composition of multispecies biofilms should be a key consideration when determining antimicrobial treatments.
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Affiliation(s)
- Jiajun Dong
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Luhan Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Liying Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Yuqiang Xiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Yabin Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Youbao Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
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37
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Wang W, Rahman A, Kang S, Vikesland PJ. Investigation of the Influence of Stress on Label-Free Bacterial Surface-Enhanced Raman Spectra. Anal Chem 2023; 95:3675-3683. [PMID: 36757218 DOI: 10.1021/acs.analchem.2c04636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Label-free surface-enhanced Raman spectroscopy (SERS) has been proposed as a promising bacterial detection technique. However, the quality of the collected bacterial spectra can be affected by the time between sample acquisition and the SERS measurement. This study evaluated how storage stress stimuli influence the label-free SERS spectra of Pseudomonas syringae samples stored in phosphate buffered saline. The results indicate that when faced with nutrient limitations and changes in osmatic pressure, samples at room temperature (25 °C) exhibit more significant spectral changes than those stored at cold temperature (4 °C). At higher temperatures, bacterial communities secrete extracellular biomolecules that induce programmed cell death and result in increases in the supernatant SERS signals. Surviving cells consume cellular components to support their metabolism, thus leading to measurable declines in cell SERS intensity. Two-dimensional correlation spectroscopy analysis suggests that cellular component signatures decline sequentially in the following order: proteins, nucleic acids, and lipids. Extracellular nucleic acids, proteins, and carbohydrates are secreted in turn. After subtracting the SERS changes resulting from storage, we evaluated bacterial response to viral infection. P. syringae SERS profile changes enable accurate bacteriophage Phi6 quantification over the range of 104-1010 PFU/mL. The results indicate that storage conditions impact bacterial label-free SERS signals and that such influences need to be accounted for and if possible avoided when detecting bacteria or evaluating bacterial response to stress stimuli.
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Affiliation(s)
- Wei Wang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Asifur Rahman
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Seju Kang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Virginia Tech, Blacksburg, Virginia 24061, United States
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38
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Flemming HC, van Hullebusch ED, Neu TR, Nielsen PH, Seviour T, Stoodley P, Wingender J, Wuertz S. The biofilm matrix: multitasking in a shared space. Nat Rev Microbiol 2023; 21:70-86. [PMID: 36127518 DOI: 10.1038/s41579-022-00791-0] [Citation(s) in RCA: 156] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 01/20/2023]
Abstract
The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.
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Affiliation(s)
- Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | | | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Thomas Seviour
- Aarhus University Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.,Department of Orthopaedics, The Ohio State University, Columbus, OH, USA
| | - Jost Wingender
- University of Duisburg-Essen, Biofilm Centre, Department of Aquatic Microbiology, Essen, Germany
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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Nyanasegran PK, Nathan S, Firdaus-Raih M, Muhammad NAN, Ng CL. Biofilm Signaling, Composition and Regulation in Burkholderia pseudomallei. J Microbiol Biotechnol 2023; 33:15-27. [PMID: 36451302 PMCID: PMC9899790 DOI: 10.4014/jmb.2207.07032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 12/04/2022]
Abstract
The incidence of melioidosis cases caused by the gram-negative pathogen Burkholderia pseudomallei (BP) is seeing an increasing trend that has spread beyond its previously known endemic regions. Biofilms produced by BP have been associated with antimicrobial therapy limitation and relapse melioidosis, thus making it urgently necessary to understand the mechanisms of biofilm formation and their role in BP biology. Microbial cells aggregate and enclose within a self-produced matrix of extracellular polymeric substances (EPSs) to form biofilm. The transition mechanism of bacterial cells from planktonic state to initiate biofilm formation, which involves the formation of surface attachment microcolonies and the maturation of the biofilm matrix, is a dynamic and complex process. Despite the emerging findings on the biofilm formation process, systemic knowledge on the molecular mechanisms of biofilm formation in BP remains fractured. This review provides insights into the signaling systems, matrix composition, and the biosynthesis regulation of EPSs (exopolysaccharide, eDNA and proteins) that facilitate the formation of biofilms in order to present an overview of our current knowledge and the questions that remain regarding BP biofilms.
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Affiliation(s)
| | - Sheila Nathan
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia,Corresponding author Phone: +03 8921 4561 Fax: +603 8921 3398 E-mail:
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40
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Kutsuno S, Hayashi I, Yu L, Yamada S, Hisatsune J, Sugai M. Non-deacetylated poly- N-acetylglucosamine-hyperproducing Staphylococcus aureus undergoes immediate autoaggregation upon vortexing. Front Microbiol 2023; 13:1101545. [PMID: 36699608 PMCID: PMC9868172 DOI: 10.3389/fmicb.2022.1101545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
Biofilms are microbial communities of cells embedded in a matrix of extracellular polymeric substances generated and adhering to each other or to a surface. Cell aggregates formed in the absence of a surface and floating pellicles that form biofilms at the air-liquid interface are also considered to be a type of biofilm. Staphylococcus aureus is a well-known cause of biofilm infections and high-molecular-weight polysaccharides, poly-N-acetylglucosamine (PNAG) is a main constituent of the biofilm. An icaADBC operon comprises major machinery to synthesize and extracellularly secrete PNAG. Extracellular PNAG is partially deacetylated by IcaB deacetylase, and the positively charged PNAG hence interacts with negatively charged cell surface to form the major component of biofilm. We previously reported a new regulator of biofilm (Rob) and demonstrated that Rob binds to a unique 5-bp motif, TATTT, present in intergenic region between icaADBC operon and its repressor gene icaR in Yu et al. The deletion of the 5-bp motif induces excessive adherent biofilm formation. The real function of the 5-bp motif is still unknown. In an attempt to isolate the 5-bp motif deletion mutant, we isolated several non-adherent mutants. They grew normally in turbid broth shaking culture but immediately auto-aggregated upon weak vortexing and sedimented as a lump resulting in a clear supernatant. Whole genome sequencing of the mutants identified they all carried mutations in icaB in addition to deletion of the 5-bp motif. Purification and molecular characterization of auto-aggregating factor in the culture supernatant of the mutant identified that the factor was a massively produced non-deacetylated PNAG. Therefore, we created a double deficient strain of biofilm inhibitory factors (5-bp motif, icaR, rob) and icaB to confirm the aggregation phenomenon. This peculiar phenomenon was only observed in Δ5bpΔicaB double mutant but not in ΔicaR ΔicaB or ΔrobΔicaB mutant. This study explains large amount of extracellularly produced non-deacetylated PNAG by Δ5bpΔicaB double mutation induced rapid auto-aggregation of S. aureus cells by vortexing. This phenomenon indicated that Staphylococcus aureus may form biofilms that do not adhere to solid surfaces and we propose this as a new mechanism of non-adherent biofilm formation of S. aureus.
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Affiliation(s)
- Shoko Kutsuno
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan,Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Ikue Hayashi
- Research Facility, Hiroshima University Faculty of Dentistry, Hiroshima, Japan
| | - Liansheng Yu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan,Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Sakuo Yamada
- Department of Medical Technology, Faculty of Health Sciences & Technology, Kawasaki University of Medical Welfare, Okayama, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan,Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan,Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan,*Correspondence: Motoyuki Sugai,
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41
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Mues N, Martin RJ, Alam R, Schaunaman N, Dimasuay KG, Kolakowski C, Wright CJ, Zheng L, Chu HW. Bacterial DNA amplifies neutrophilic inflammation in IL-17-exposed airways. ERJ Open Res 2023; 9:00474-2022. [PMID: 36699649 PMCID: PMC9868970 DOI: 10.1183/23120541.00474-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Background Neutrophilic asthma (NA) is associated with increased airway interleukin (IL)-17 and abnormal bacterial community such as dominance of nontypeable Haemophilus influenzae (NTHi), particularly during asthma exacerbations. Bacteria release various products including DNA, but whether they cooperate with IL-17 in exaggerating neutrophilic inflammation is unclear. We sought to investigate the role of bacteria-derived DNA in airway neutrophilic inflammation related to IL-17-high asthma and underlying mechanisms (e.g. Toll-like receptor 9 (TLR9)/IL-36γ signalling axis). Methods Bacterial DNA, IL-8 and IL-36γ were measured in bronchoalveolar lavage fluid (BALF) of people with asthma and healthy subjects. The role of co-exposure to IL-17 and bacterial DNA or live bacteria in neutrophilic inflammation, and the contribution of the TLR9/IL-36γ signalling axis, were determined in cultured primary human airway epithelial cells and alveolar macrophages, and mouse models. Results Bacterial DNA levels were increased in asthma BALF, which positively correlated with IL-8 and neutrophil levels. Moreover, IL-36γ increased in BALF of NA patients. Bacterial DNA or NTHi infection under an IL-17-high setting amplified IL-8 production and mouse lung neutrophilic inflammation. DNase I treatment in IL-17-exposed and NTHi-infected mouse lungs reduced neutrophilic inflammation. Mechanistically, bacterial DNA-mediated amplification of neutrophilic inflammation is in part dependent on the TLR9/IL-36γ signalling axis. Conclusions Bacterial DNA amplifies airway neutrophilic inflammation in an IL-17-high setting partly through the TLR9 and IL-36γ signalling axis. Our novel findings may offer several potential therapeutic targets including TLR9 antagonists, IL-36γ neutralising antibodies and DNase I to reduce asthma severity associated with exaggerated airway neutrophilic inflammation.
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Affiliation(s)
- Nastaran Mues
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | | | - Rafeul Alam
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | | | | | | | - Clyde J. Wright
- Department of Pediatrics, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Lijun Zheng
- Department of Pediatrics, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Hong Wei Chu
- Department of Medicine, National Jewish Health, Denver, CO, USA
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42
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Jiao X, Guo W, Li X, Yao F, Zeng M, Yuan Y, Guo X, Wang M, Xie QD, Cai L, Yu F, Yu P, Xia Y. New insight into the microbiome, resistome, and mobilome on the dental waste water in the context of heavy metal environment. Front Microbiol 2023; 14:1106157. [PMID: 37152760 PMCID: PMC10157219 DOI: 10.3389/fmicb.2023.1106157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Object Hospital sewage have been associated with incorporation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into microbes, which is considered as a key indicator for the spread of antimicrobial resistance (AMR). The compositions of dental waste water (DWW) contain heavy metals, the evolution of AMR and its effects on the water environment in the context of heavy metal environment have not been seriously investigated. Thus, our major aims were to elucidate the evolution of AMR in DWW. Methods DWW samples were collected from a major dental department. The presence of microbial communities, ARGs, and MGEs in untreated and treated (by filter membrane and ozone) samples were analyzed using metagenomics and bioinformatic methods. Results DWW-associated resistomes included 1,208 types of ARGs, belonging to 29 antibiotic types/subtypes. The most abundant types/subtypes were ARGs of multidrug resistance and of antibiotics that were frequently used in the clinical practice. Pseudomonas putida, Pseudomonas aeruginosa, Chryseobacterium indologenes, Sphingomonas laterariae were the main bacteria which hosted these ARGs. Mobilomes in DWW consisted of 93 MGE subtypes which belonged to 8 MGE types. Transposases were the most frequently detected MGEs which formed networks of communications. For example, ISCrsp1 and tnpA.5/4/11 were the main transposases located in the central hubs of a network. These significant associations between ARGs and MGEs revealed the strong potential of ARGs transmission towards development of antimicrobial-resistant (AMR) bacteria. On the other hand, treatment of DWW using membranes and ozone was only effective in removing minor species of bacteria and types of ARGs and MGEs. Conclusion DWW contained abundant ARGs, and MGEs, which contributed to the occurrence and spread of AMR bacteria. Consequently, DWW would seriously increase environmental health concerns which may be different but have been well-documented from hospital waste waters.
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Affiliation(s)
- Xiaoyang Jiao
- College of Medicine, Shantou University, Shantou, China
| | - Wenyan Guo
- Department of Clinical Laboratory, First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xin Li
- College of Medicine, Shantou University, Shantou, China
| | - Fen Yao
- Department of Pharmacology, College of Medicine, Shantou University, Shantou, China
| | - Mi Zeng
- College of Medicine, Shantou University, Shantou, China
| | - Yumeng Yuan
- College of Medicine, Shantou University, Shantou, China
| | - Xiaoling Guo
- College of Medicine, Shantou University, Shantou, China
| | - Meimei Wang
- College of Medicine, Shantou University, Shantou, China
| | - Qing Dong Xie
- College of Medicine, Shantou University, Shantou, China
| | - Leshan Cai
- Department of Clinical Laboratory, First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Feiyuan Yu
- College of Medicine, Shantou University, Shantou, China
| | - Pen Yu
- Department of Clinical Laboratory, First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yong Xia
- Department of Clinical Laboratory, First Affiliated Hospital of Shantou University Medical College, Shantou, China
- *Correspondence: Yong Xia,
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Updated Review on the Mechanisms of Pathogenicity in Mycobacterium abscessus, a Rapidly Growing Emerging Pathogen. Microorganisms 2022; 11:microorganisms11010090. [PMID: 36677382 PMCID: PMC9866562 DOI: 10.3390/microorganisms11010090] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
In recent years, Mycobacterium abscessus has appeared as an emerging pathogen, with an increasing number of disease cases reported worldwide that mainly occur among patients with chronic lung diseases or impaired immune systems. The treatment of this pathogen represents a challenge due to the multi-drug-resistant nature of this species and its ability to evade most therapeutic approaches. However, although predisposing host factors for disease are well known, intrinsic pathogenicity mechanisms of this mycobacterium are still not elucidated. Like other mycobacteria, intracellular invasiveness and survival inside different cell lines are pathogenic factors related to the ability of M. abscessus to establish infection. Some of the molecular factors involved in this process are well-known and are present in the mycobacterial cell wall, such as trehalose-dimycolate and glycopeptidolipids. The ability to form biofilms is another pathogenic factor that is essential for the development of chronic disease and for promoting mycobacterial survival against the host immune system or different antibacterial treatments. This capability also seems to be related to glycopeptidolipids and other lipid molecules, and some studies have shown an intrinsic relationship between both pathogenic mechanisms. Antimicrobial resistance is also considered a mechanism of pathogenicity because it allows the mycobacterium to resist antimicrobial therapies and represents an advantage in polymicrobial biofilms. The recent description of hyperpathogenic strains with the potential interhuman transmission makes it necessary to increase our knowledge of pathogenic mechanisms of this species to design better therapeutic approaches to the management of these infections.
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Moshynets OV, Pokholenko I, Iungin O, Potters G, Spiers AJ. eDNA, Amyloid Fibers and Membrane Vesicles Identified in Pseudomonas fluorescens SBW25 Biofilms. Int J Mol Sci 2022; 23:ijms232315096. [PMID: 36499433 PMCID: PMC9738004 DOI: 10.3390/ijms232315096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas fluorescens SBW25 is a model soil- and plant-associated bacterium capable of forming a variety of air-liquid interface biofilms in experimental microcosms and on plant surfaces. Previous investigations have shown that cellulose is the primary structural matrix component in the robust and well-attached Wrinkly Spreader biofilm, as well as in the fragile Viscous Mass biofilm. Here, we demonstrate that both biofilms include extracellular DNA (eDNA) which can be visualized using confocal laser scanning microscopy (CLSM), quantified by absorbance measurements, and degraded by DNase I treatment. This eDNA plays an important role in cell attachment and biofilm development. However, exogenous high-molecular-weight DNA appears to decrease the strength and attachment levels of mature Wrinkly Spreader biofilms, whereas low-molecular-weight DNA appears to have little effect. Further investigation with CLSM using an amyloid-specific fluorophore suggests that the Wrinkly Spreader biofilm might also include Fap fibers, which might be involved in attachment and contribute to biofilm strength. The robust nature of the Wrinkly Spreader biofilm also allowed us, using MALDI-TOF mass spectrometry, to identify matrix-associated proteins unable to diffuse out of the structure, as well as membrane vesicles which had a different protein profile compared to the matrix-associated proteins. CLSM and DNase I treatment suggest that some vesicles were also associated with eDNA. These findings add to our understanding of the matrix components in this model pseudomonad, and, as found in other biofilms, biofilm-specific products and material from lysed cells contribute to these structures through a range of complex interactions.
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Affiliation(s)
- Olena V. Moshynets
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Ianina Pokholenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Olga Iungin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Kyiv National University of Technologies and Design, 01011 Kyiv, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, 2030 Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, 2000 Antwerp, Belgium
- Correspondence:
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
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Overcoming Antibiotic Resistance with Novel Paradigms of Antibiotic Selection. Microorganisms 2022; 10:microorganisms10122383. [PMID: 36557636 PMCID: PMC9781420 DOI: 10.3390/microorganisms10122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Conventional antimicrobial susceptibility tests, including phenotypic and genotypic methods, are insufficiently accurate and frequently fail to identify effective antibiotics. These methods predominantly select therapies based on the antibiotic response of only the lead bacterial pathogen within pure bacterial culture. However, this neglects the fact that, in the majority of human infections, the lead bacterial pathogens are present as a part of multispecies communities that modulate the response of these lead pathogens to antibiotics and that multiple pathogens can contribute to the infection simultaneously. This discrepancy is a major cause of the failure of antimicrobial susceptibility tests to detect antibiotics that are effective in vivo. This review article provides a comprehensive overview of the factors that are missed by conventional antimicrobial susceptibility tests and it explains how accounting for these methods can aid the development of novel diagnostic approaches.
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González-Plaza JJ, Furlan C, Rijavec T, Lapanje A, Barros R, Tamayo-Ramos JA, Suarez-Diez M. Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels. Front Microbiol 2022; 13:1006946. [PMID: 36519168 PMCID: PMC9744117 DOI: 10.3389/fmicb.2022.1006946] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/02/2022] [Indexed: 08/31/2023] Open
Abstract
The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.
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Affiliation(s)
- Juan José González-Plaza
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Rocío Barros
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
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Bairoliya S, Goel A, Mukherjee M, Koh Zhi Xiang J, Cao B. Monochloramine Induces Release of DNA and RNA from Bacterial Cells: Quantification, Sequencing Analyses, and Implications. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15791-15804. [PMID: 36215406 DOI: 10.1021/acs.est.2c06632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Monochloramine (MCA) is a widely used secondary disinfectant to suppress microbial growth in drinking water distribution systems. In monochloraminated drinking water, a significant amount of extracellular DNA (eDNA) has been reported, which has many implications ranging from obscuring DNA-based drinking water microbiome analyses to posing potential health concerns. To address this, it is imperative for us to know the origin of the eDNA in drinking water. Using Pseudomonas aeruginosa as a model organism, we report for the first time that MCA induces the release of nucleic acids from both biofilms and planktonic cells. Upon exposure to 2 mg/L MCA, massive release of DNA from suspended cells in both MilliQ water and 0.9% NaCl was directly visualized using live cell imaging in a CellASIC ONIX2 microfluidic system. Exposing established biofilms to MCA also resulted in DNA release from the biofilms, which was confirmed by increased detection of eDNA in the effluent. Intriguingly, massive release of RNA was also observed, and the extracellular RNA (eRNA) was also found to persist in water for days. Sequencing analyses of the eDNA revealed that it could be used to assemble the whole genome of the model organism, while in the water, certain fragments of the genome were more persistent than others. RNA sequencing showed that the eRNA contains non-coding RNA and mRNA, implying its role as a possible signaling molecule in environmental systems and a snapshot of the past metabolic state of the bacterial cells.
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Affiliation(s)
- Sakcham Bairoliya
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
| | - Apoorva Goel
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
| | - Jonas Koh Zhi Xiang
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
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48
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Guillaume O, Butnarasu C, Visentin S, Reimhult E. Interplay between biofilm microenvironment and pathogenicity of Pseudomonas aeruginosa in cystic fibrosis lung chronic infection. Biofilm 2022; 4:100089. [PMID: 36324525 PMCID: PMC9618985 DOI: 10.1016/j.bioflm.2022.100089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
Pseudomonas aeruginosa (PA) is a highly, if not the most, versatile microorganism capable of colonizing diverse environments. One of the niches in which PA is able to thrive is the lung of cystic fibrosis (CF) patients. Due to a genetic aberration, the lungs of CF-affected patients exhibit impaired functions, rendering them highly susceptible to bacterial colonization. Once PA attaches to the epithelial surface and transitions to a mucoid phenotype, the infection becomes chronic, and antibiotic treatments become inefficient. Due to the high number of affected people and the severity of this infection, CF-chronic infection is a well-documented disease. Still, numerous aspects of PA CF infection remain unclear. The scientific reports published over the last decades have stressed how PA can adapt to CF microenvironmental conditions and how its surrounding matrix of extracellular polymeric substances (EPS) plays a key role in its pathogenicity. In this context, it is of paramount interest to present the nature of the EPS together with the local CF-biofilm microenvironment. We review how the PA biofilm microenvironment interacts with drugs to contribute to the pathogenicity of CF-lung infection. Understanding why so many drugs are inefficient in treating CF chronic infection while effectively treating planktonic PA is essential to devising better therapeutic targets and drug formulations.
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Affiliation(s)
- Olivier Guillaume
- 3D Printing and Biofabrication Group, Institute of Materials Science and Technology, TU Wien (Technische Universität Wien), Getreidemarkt 9/308, 1060, Vienna, Austria,Austrian Cluster for Tissue Regeneration, Austria,Corresponding author. 3D Printing and Biofabrication Group, Institute of Materials Science and Technology, TU Wien (Technische Universität Wien), Getreidemarkt 9/308, 1060, Vienna, Austria.
| | - Cosmin Butnarasu
- Department of Molecular Biotechnology and Health Science, University of Turin, Turin, 10135, Italy
| | - Sonja Visentin
- Department of Molecular Biotechnology and Health Science, University of Turin, Turin, 10135, Italy
| | - Erik Reimhult
- Institute of Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, 1190, Vienna, Austria
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Liu S, Le Mauff F, Sheppard DC, Zhang S. Filamentous fungal biofilms: Conserved and unique aspects of extracellular matrix composition, mechanisms of drug resistance and regulatory networks in Aspergillus fumigatus. NPJ Biofilms Microbiomes 2022; 8:83. [PMID: 36261442 PMCID: PMC9581972 DOI: 10.1038/s41522-022-00347-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
The filamentous fungus Aspergillus fumigatus is an ubiquitous mold that can cause invasive pulmonary infections in immunocompromised patients. Within the lung, A. fumigatus forms biofilms that can enhance resistance to antifungals and immune defenses, highlighting the importance of defining the mechanisms underlying biofilm development and associated emergent properties. A. fumigatus biofilms display a morphology and architecture that is distinct from bacterial and yeast biofilms. Moreover, A. fumigatus biofilms display unique characteristics in the composition of their extracellular matrix (ECM) and the regulatory networks governing biofilm formation. This review will discuss our current understanding of the form and function of A. fumigatus biofilms, including the unique components of ECM matrix, potential drug resistance mechanisms, the regulatory networks governing A. fumigatus biofilm formation, and potential therapeutics targeting these structures.
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Affiliation(s)
- Shuai Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Francois Le Mauff
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Infectious Disease and Immunity in Global Health, Research Institute of McGill University Health Center, Montreal, QC, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada
| | - Donald C Sheppard
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, QC, Canada. .,Infectious Disease and Immunity in Global Health, Research Institute of McGill University Health Center, Montreal, QC, Canada. .,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| | - Shizhu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
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50
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Yangyanqiu W, Shuwen H. Bacterial DNA involvement in carcinogenesis. Front Cell Infect Microbiol 2022; 12:996778. [PMID: 36310856 PMCID: PMC9600336 DOI: 10.3389/fcimb.2022.996778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/27/2022] [Indexed: 10/29/2023] Open
Abstract
The incidence of cancer is high worldwide, and biological factors such as viruses and bacteria play an important role in the occurrence of cancer. Helicobacter pylori, human papillomavirus, hepatitis B viruses and other organisms have been identified as carcinogens. Cancer is a disease driven by the accumulation of genome changes. Viruses can directly cause cancer by changing the genetic composition of the human body, such as cervical cancer caused by human papillomavirus DNA integration and liver cancer caused by hepatitis B virus DNA integration. Recently, bacterial DNA has been found around cancers such as pancreatic cancer, breast cancer and colorectal cancer, and the idea that bacterial genes can also be integrated into the human genome has become a hot topic. In the present paper, we reviewed the latest phenomenon and specific integration mechanism of bacterial DNA into the human genome. Based on these findings, we also suggest three sources of bacterial DNA in cancers: bacterial DNA around human tissues, free bacterial DNA in bacteremia or sepsis, and endogenous bacterial DNA in the human genome. Clarifying the theory that bacterial DNA integrates into the human genome can provide a new perspective for cancer prevention and treatment.
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Affiliation(s)
- Wang Yangyanqiu
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
- Graduate School of Medical college of Zhejiang University, Hangzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, China
| | - Han Shuwen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
- Graduate School of Medical college of Zhejiang University, Hangzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, China
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